Try a (dirty) fix to the i-pi neighbor list update problem

src/MISC/fix_ipi.cpp

@@ -30,6 +30,7 @@
 #include "update.h"
 
 #include <cstring>
+#include <iostream>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -363,10 +364,36 @@ void FixIPI::initial_integrate(int /*vflag*/)
   // has to be be done before invoking Irregular::migrate_atoms()
   //   since it requires atoms be inside simulation box
 
+
+  if (neighbor->ncalls == 0) {
+    
   if (domain->triclinic) domain->x2lamda(atom->nlocal);
-  domain->pbc();
-  domain->reset_box();
-  if (domain->triclinic) domain->lamda2x(atom->nlocal);
+    domain->pbc();
+    domain->reset_box();
+    if (domain->triclinic) domain->lamda2x(atom->nlocal);
+  } else { // for some reason this fails if it's called on the first step.
+    // "unwraps" the trajectory because we have no guarantee of what has happened 
+    // server-side to the atoms folding
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        x[i][0] -= neighbor->xhold[i][0];
+        x[i][1] -= neighbor->xhold[i][1];
+        x[i][2] -= neighbor->xhold[i][2];
+      }
+    }
+    if (domain->triclinic) domain->x2lamda(atom->nlocal);
+    domain->pbc();
+    domain->reset_box();
+    if (domain->triclinic) domain->lamda2x(atom->nlocal);
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        x[i][0] += neighbor->xhold[i][0];
+        x[i][1] += neighbor->xhold[i][1];
+        x[i][2] += neighbor->xhold[i][2];
+      }
+    }
+  }
+  /**/
 
   // move atoms to new processors via irregular()
   // only needed if migrate_check() says an atom moves to far

src/neighbor.cpp

@@ -53,6 +53,7 @@
 
 #include <cmath>
 #include <cstring>
+#include <iostream>
 
 using namespace LAMMPS_NS;
 using namespace NeighConst;
@@ -2384,12 +2385,16 @@ int Neighbor::check_distance()
     dely = x[i][1] - xhold[i][1];
     delz = x[i][2] - xhold[i][2];
     rsq = delx*delx + dely*dely + delz*delz;
-    if (rsq > deltasq) flag = 1;
+    if (rsq > deltasq) {
+      std::cout<<"jump: "<< rsq<<std::endl;
+      flag = 1;
+    }
   }
 
   int flagall;
   MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
   if (flagall && ago == MAX(every,delay)) ndanger++;
+  std::cout<<" neigh update flags "<< flagall<< "  "<< ago << "  "<<ndanger<<std::endl;
   return flagall;
 }
 

src/neighbor.h

@@ -58,7 +58,8 @@ class Neighbor : protected Pointers {
 
   double *bboxlo, *bboxhi;    // ptrs to full domain bounding box
                               // different for orthog vs triclinic
-
+  double **xhold;    // atom coords at last neighbor build
+  int maxhold;       // size of xhold array
   // exclusion info, used by NeighPair
 
   int exclude;    // 0 if no type/group exclusions, 1 if yes
@@ -190,8 +191,8 @@ class Neighbor : protected Pointers {
 
   double triggersq;    // trigger = build when atom moves this dist
 
-  double **xhold;    // atom coords at last neighbor build
-  int maxhold;       // size of xhold array
+  //double **xhold;    // atom coords at last neighbor build
+  //int maxhold;       // size of xhold array
 
   int boxcheck;                           // 1 if need to store box size
   double boxlo_hold[3], boxhi_hold[3];    // box size at last neighbor build